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Protein Structure Comparison by Alignment of Distance Matrices
Abstract
With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.
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“The templates were pairwise structurally aligned according to DALILite (41,42), using HIF-2 α as a reference. The sequence alignments were obtained by CLUSTALW (43), and the result was confirmed using the Align-2D command within the MODELLER program (37-39).”
From Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis (2007) · cites this paper as [41]
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RENWICK, S. B., Snell, K., & Baumann, U. (1998) · Structure · doi:10.1016/s0969-2126(98)00112-9 · Cited by 178
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“The tyrosine of 2.0 Å (210 residues) and 1.8 Å (218 residues), respecphosphatase activity was measured using a tyrosine phosphorytively (Holm and Sander, 1993; Barford et al., 1994;lated peptide derived from human hirudim in the presence and abStuckey et al., 1994).”
MethodInfluentialDrosophila kelch motif is derived from a common enzyme fold
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“A search for structural homologues by DALI (Holm and Sander, 1993) finds no close relatives of LC20.”
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Protein structure similarities
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Structural determinants in the sequences of immunoglobulin variable domain 1 1Edited by A. R. Fersht
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“…similarity is © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd, Molecular Microbiology, 63, 139–149 present, a Dali search (Holm and Sander, 1993) reveals that the IsdA NEAT domain fold is similar to that of the clathrin adapter appendage superfamily (2.9 Å r.m.s.d.…”
BackgroundInfluentialRamasubbu, N., Thomas, L. M., Ragunath, C., & Kaplan, J. B. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.03.082 · Cited by 176
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Goldman, D., Istrail, S., & Papadimitriou, C. H. (2003) · Annual Symposium on Foundations of Computer Science · doi:10.1109/sffcs.1999.814624 · Cited by 170
“Several measures of protein structure similarity have been proposed and used over the past few years, attempting to assign to each pair of proteins a distance, presumably capturing the extent to which the two proteins \resemble" each other in structure, origin, and function [17, 7, 34, 8, 28, 9, 16, 25, 27, 30, 29, 22…”
BackgroundMethodStructure of the formate transporter FocA reveals a pentameric aquaporin-like channel
Wang, Y., Huang, Y., Wang, J., Cheng, C., Huang, W., Lu, P., Xu, Y., Wang, P., Yan, N., & Shi, Y. (2009) · Nature · doi:10.1038/nature08610 · Cited by 173
Structure and Biological Activities of Beta Toxin from Staphylococcus aureus
Huseby, M. J., Shi, K., Brown, C. K., Digre, J., Mengistu, F., Seo, K. S., Bohach, G. A., Schlievert, P. M., Ohlendorf, D. H., & Earhart, C. A. (2007) · Journal of Bacteriology · doi:10.1128/jb.00741-07 · Cited by 173
“The proteins which are most structurally homologous to beta toxin, aside from the SMases, as revealed by a DALI (14) and SSM (15) search, are human endonuclease HAP1 (PDB entry 1bix; RMSD over 221 C s, 3.3 Å), E. coli endonuclease III (PDB entry 1ako; RMSD over 221 C s, 3.5 Å), the endonuclease domain of human Line-1…”
BackgroundInfluentialBiochemical and Structural Analysis of Substrate Specificity of a Phenylalanine Ammonia-Lyase
Jun, S., Sattler, S. A., Cortez, G. S., Vermerris, W., Sattler, S. E., & Kang, C. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01608 · Cited by 175
“In addition, a chain fold search using DALI (Holm and Sander, 1993) was performed using the atomic coordinates of SbPAL1 to identify closely related structural homologs in the same PDB.”
MethodInfluentialChantalat, L., Leroy, D., Filhol, O., Nueda, A., Benítez, M. J., CHAMBAZ, E. M., Cochet, C., & Dideberg, O. (1999) · The EMBO Journal · doi:10.1093/emboj/18.11.2930 · Cited by 180
“An analysis performed using DALI (Holm and Sander, 1993), involving searches with the entire molecule, showed no structural homology with other known proteins.”
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“Using Dali structure alignments (27), this domain”
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BackgroundStructural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
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A Model for Statistical Significance of Local Similarities in Structure
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Deivanayagam, C. C. S., Rich, R. L., Carson, M., Owens, R. T., Danthuluri, S., Bice, T., Höök, M., & Narayana, S. V. L. (2000) · Structure · doi:10.1016/s0969-2126(00)00081-2 · Cited by 165
“Three-dimensional alignment with DALI In a comparison of D1 with the three-dimensional (3D) structures of other protein structures present in the Protein Data Bank (PDB), the DALI program [ 23 ,24] generated the best fit with the intercellular cell adhesion molecule 2 (ICAM-2) fragment followed by coagulation factor f…”
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“The templates were pairwise structurally aligned according to DALILite (41,42), using HIF-2α as a reference.”
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Romanowski, M. J., Soccio, R. E., Breslow, J. L., & Burley, S. K. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052140699 · Cited by 162
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Binda, C., Coda, A., Angelini, R., Federico, R., Ascenzi, P., & Mattevi, A. (1999) · Structure · doi:10.1016/s0969-2126(99)80037-9 · Cited by 162
Conte, M. R., Grüne, T., Ghuman, J., Kelly, G. P., Ladas, A., Matthews, S., & Curry, S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.12.3132 · Cited by 160
X-ray crystal structure of IRF-3 and its functional implications
Takahasi, K., Suzuki, N. N., Horiuchi, M., Mori, M., Suhara, W., Okabe, Y., Fukuhara, Y., Terasawa, H., Akira, S., Fujita, T., et al. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1001 · Cited by 162
“Notably, IRF-3 175C is topologically and structurally similar to the Mad homology domain 2 (MH2 domain) of the Smad family (according to searches using Dal”
Nagem, R. A. P., Rojas, A. L., Golubev, A. M., et al. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.09.024 · Cited by 162
Structure of the RNA Polymerase Domain of E. coli Primase
Keck, J. L., Roche, D. D., Lynch, A. S., & Berger, J. M. (2000) · Science · doi:10.1126/science.287.5462.2482 · Cited by 161
The structure of ActVA‐Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis
Sciara, G., Kendrew, S. G., Miele, A. E., Marsh, E. N. G., Federici, L., Malatesta, F., Schimperna, G., Savino, C., & Vallone, B. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg031 · Cited by 162
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Takagi, H., Kakuta, Y., Okada, T., et al. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb911 · Cited by 161
“Despite this simple architecture of aRelE, structural homology searches in the Protein Data Bank using the Dali serve”
MethodModolo, L. V., Li, L., Pan, H., et al. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.08.017 · Cited by 161
Structure and Mechanism of mRNA Cap (Guanine-N7) Methyltransferase
Fàbrega, C., Hausmann, S., Shen, V., Shuman, S., & Lima, C. D. (2004) · Molecular Cell · doi:10.1016/s1097-2765(03)00522-7 · Cited by 161
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Structural and mechanistic mapping of a unique fumarate reductase.
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Bacterial actin MreB assembles in complex with cell shape protein RodZ
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“In fact, the DALI search (Holm and Sander, 1993) listed only putative DNA-interacting proteins, some of which were classified as HTH-type transcriptional regulators or belonged to the XRE family of transcription factors.”
BackgroundBolam, D. N., Roberts, S. M., Proctor, M. R., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607897104 · Cited by 158
Structural basis of the recognition of the dishevelled DEP domain in the Wnt signaling pathway.
Zheng, J., Wong, H. C., Mao, J., Nguyen, J. T., Srinivas, S., Zhang, W., Liu, B., Li, L., & Wu, D. (2000) · Nature Structural Biology · doi:10.1038/82047 · Cited by 157
Structural Basis of 2C TCR Allorecognition of H-2Ld Peptide Complexes
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Metadata
- Authors
- Holm, L., & Sander, C.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1993-09
- Volume
- 233
- Issue
- 1
- Pages
- 123-138
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2022058405
- Cited by
- 3,984
- References
- 0
- Citations by year
- 2026: 23 · 2025: 31 · 2024: 22 · 2023: 22 · 2022: 28 · 2021: 27 · 2020: 53 · 2019: 50 · 2018: 45 · 2017: 42 · 2016: 53 · 2015: 65 · 2014: 73 · 2013: 106 · 2012: 98
- FWCI
- 15.32
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- protein structure comparison, Dali, Monte Carlo optimization, structural similarity, protein fold classification, structural core, colicin A, globin, lambda repressor, sequence gaps
- MeSH terms
- Actins, Algorithms, Amino Acid Sequence, Colicins, DNA-Binding Proteins, Globins, Heat-Shock Proteins, Hexokinase, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Muramidase, Software, Reproducibility of Results, Cluster Analysis, Sequence Alignment, Sequence Homology, Amino Acid, Protein Structure, Secondary, Protein Structure, Tertiary
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